Question9 Looking at gene A in the figure below, which start site do you believe

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Question9 Looking at gene A in the figure below, which start site do you believe is the best selection based on the information provided by the coding potential map When examining start sites, the first important thing to do is to determine whether the gene is in the FORWARD or REVERSE direction. For gene A, there is a small down tick mark at the end of the line in the middle of the screen on the right side so this means we will be reading this gene from left to right. A gene with a start on the left and a stop on the right is read in the FORWARD direction. Let's add one more piece of information the thin line in the center of the figure represents the longest possible gene call. If you look carefully, you see that the thin line extends from the first possible start site to the stop codon. The thick black line at the bottom indicates the gene call that the computer algorithm prefers. In many cases, the 2 agree. The computer program often likes to call the longest possible gene call. But sometimes, the computer algorithm does not think the longest gene call is the best because of other things like coding potential data. Which start site do you think is the best for gene A in the figure? C D ZUUU 1600 600 680 760 1000

Explanation / Answer

Ans 1. Since the gene is in forward direction because the downward tick mark is at the extreme right. It determines that the start codon will be at the left side and the stop codon will be at the right side. so a site upstream to the 800 will be the best to complete the open reading frame (ORF). So the most correct option will be 760. However the other sites like 600 and 680 are further more downstream but they far more distant than the origin that is 800, so they may cause the hinderance in the initiation of the process. There is a lot noise in the area below 700, so it should be avoided. That’s why the section from where the peaks are sharp is chosen as the start point for the gene A.

Ans 2. In this case the downward tick mark is in the left end of the graph, this means that the gene is in reverse direction. So the start point near the 38000 will be the best start site for this gene. We know that the forward genes are best to be chosen for longest gene call. But more right to the 38000 there is no sharp peak which let us to reject the other options to be considered. SO 38000 is the most correct option.

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